Package: cfTools 1.5.0
Ran Hu
cfTools: Informatics Tools for Cell-Free DNA Study
The cfTools R package provides methods for cell-free DNA (cfDNA) methylation data analysis to facilitate cfDNA-based studies. Given the methylation sequencing data of a cfDNA sample, for each cancer marker or tissue marker, we deconvolve the tumor-derived or tissue-specific reads from all reads falling in the marker region. Our read-based deconvolution algorithm exploits the pervasiveness of DNA methylation for signal enhancement, therefore can sensitively identify a trace amount of tumor-specific or tissue-specific cfDNA in plasma. cfTools provides functions for (1) cancer detection: sensitively detect tumor-derived cfDNA and estimate the tumor-derived cfDNA fraction (tumor burden); (2) tissue deconvolution: infer the tissue type composition and the cfDNA fraction of multiple tissue types for a plasma cfDNA sample. These functions can serve as foundations for more advanced cfDNA-based studies, including cancer diagnosis and disease monitoring.
Authors:
cfTools_1.5.0.tar.gz
cfTools_1.5.0.zip(r-4.5)cfTools_1.5.0.zip(r-4.4)cfTools_1.5.0.zip(r-4.3)
cfTools_1.5.0.tgz(r-4.4-arm64)cfTools_1.5.0.tgz(r-4.4-x86_64)cfTools_1.5.0.tgz(r-4.3-arm64)cfTools_1.5.0.tgz(r-4.3-x86_64)
cfTools_1.5.0.tar.gz(r-4.5-noble)cfTools_1.5.0.tar.gz(r-4.4-noble)
cfTools_1.5.0.tgz(r-4.4-emscripten)cfTools_1.5.0.tgz(r-4.3-emscripten)
cfTools.pdf |cfTools.html✨
cfTools/json (API)
NEWS
| # Install 'cfTools' in R: |
| install.packages('cfTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jasminezhoulab/cftools/issues
- CancerDetector.markers - Cancer-specific marker parameter
- CancerDetector.reads - Fragment-level methylation state for cancer detection
- CpG_OB_demo - Methylation information for CpG on the original bottom strand
- CpG_OT_demo - Methylation information for CpG on the original top strand
- beta_matrix - Beta value matrix
- cfDeconvolve.markers - Tissue-specific marker parameter
- cfDeconvolve.reads - Fragment-level methylation state for tissue deconvolution
- cfSort.reads - Fragment-level methylation state for cfSort tissue deconvolution
- cfsort_markers - CfSort markers
- demo.fragment_level.meth.bed - Fragment-level methylation information
- demo.refo_frag.bed - Fragment-level information
- demo.refo_meth.bed - Methylation information on fragments
- demo.sorted.bed - Paired-end sequencing reads
- marker_index - Marker name
- markers.bed - Genomic postions of markers
- sample_type - Sample type
On BioConductor:cfTools-1.5.0(bioc 3.20)cfTools-1.4.0(bioc 3.19)
Last updated 2 months agofrom:4df84a5b51
Exports:CancerDetectorcfDeconvolvecfSortGenerateFragMethGenerateMarkerParamMergeCpGsMergePEReads
Dependencies:AnnotationDbiAnnotationHubaskpassbasiliskbasilisk.utilsBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemcfToolsDataclicpp11crayoncurlDBIdbplyrdir.expirydplyrExperimentHubfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesglueherehttrIRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixmemoisemimeopensslpillarpkgconfigplogrpngpurrrR.methodsS3R.ooR.utilsR6rappdirsRcppRcppTOMLreticulaterlangrprojrootRSQLiteS4VectorsstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectoryamlzlibbioc
